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*
*  Copyright Insight Software Consortium
*
*  Licensed under the Apache License, Version 2.0 (the "License");
*  you may not use this file except in compliance with the License.
*  You may obtain a copy of the License at
*
*         http://www.apache.org/licenses/LICENSE-2.0.txt
*
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*  distributed under the License is distributed on an "AS IS" BASIS,
*  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
*  See the License for the specific language governing permissions and
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*
*=========================================================================*/
#ifndef __itkEnhancedHistogramToTextureFeaturesFilter_h
#define __itkEnhancedHistogramToTextureFeaturesFilter_h

#include "itkHistogram.h"
#include "itkMacro.h"
#include "itkProcessObject.h"
#include "itkSimpleDataObjectDecorator.h"

/** Get built-in type.  Creates member Get"name"() (e.g., GetVisibility()); */
#define itkMacroGLCMFeatureGetter(name)                                       \
  const MeasurementObjectType * Get##name##Output() const;                      \
  \
  MeasurementType Get##name() const;

namespace itk
{
  namespace Statistics
  {
    /** \class EnhancedHistogramToTextureFeaturesFilter
    *  \brief This class computes texture feature coefficients from a grey level
    * co-occurrence matrix.
    *
    * This class computes features that summarize image texture, given a grey level
    * co-occurrence matrix (generated by a ScalarImageToCooccurrenceMatrixFilter
    * or related class).
    *
    * The features calculated are as follows (where \f$ g(i, j) \f$ is the element in
    * cell i, j of a a normalized GLCM):
    *
    * "Energy" \f$ = f_1 = \sum_{i,j}g(i, j)^2 \f$
    *
    * "Entropy" \f$ = f_2 = -\sum_{i,j}g(i, j) \log_2 g(i, j)\f$, or 0 if \f$g(i, j) = 0\f$
    *
    * "Correlation" \f$ = f_3 = \sum_{i,j}\frac{(i - \mu)(j - \mu)g(i, j)}{\sigma^2} \f$
    *
    * "Difference Moment" \f$= f_4 = \sum_{i,j}\frac{1}{1 + (i - j)^2}g(i, j) \f$
    *
    * "Inertia" \f$ = f_5 = \sum_{i,j}(i - j)^2g(i, j) \f$ (sometimes called "contrast.")
    *
    * "Cluster Shade" \f$ = f_6 = \sum_{i,j}((i - \mu) + (j - \mu))^3 g(i, j) \f$
    *
    * "Cluster Prominence" \f$ = f_7 = \sum_{i,j}((i - \mu) + (j - \mu))^4 g(i, j) \f$
    *
    * "Haralick's Correlation" \f$ = f_8 = \frac{\sum_{i,j}(i, j) g(i, j) -\mu_t^2}{\sigma_t^2} \f$
    * where \f$\mu_t\f$ and \f$\sigma_t\f$ are the mean and standard deviation of the row
    * (or column, due to symmetry) sums.
    *
    * Above, \f$ \mu =  \f$ (weighted pixel average) \f$ = \sum_{i,j}i \cdot g(i, j) =
    * \sum_{i,j}j \cdot g(i, j) \f$ (due to matrix summetry), and
    *
    * \f$ \sigma =  \f$ (weighted pixel variance) \f$ = \sum_{i,j}(i - \mu)^2 \cdot g(i, j) =
    * \sum_{i,j}(j - \mu)^2 \cdot g(i, j)  \f$  (due to matrix summetry)
    *
    * A good texture feature set to use is the Conners, Trivedi and Harlow set:
    * features 1, 2, 4, 5, 6, and 7. There is some correlation between the various
    * features, so using all of them at the same time is not necessarialy a good idea.
    *
    * NOTA BENE: The input histogram will be forcably normalized!
    * This algorithm takes three passes through the input
    * histogram if the histogram was already normalized, and four if not.
    *
    * Web references:
    *
    * http://www.cssip.uq.edu.au/meastex/www/algs/algs/algs.html
    * http://www.ucalgary.ca/~mhallbey/texture/texture_tutorial.html
    *
    * Print references:
    *
    * Haralick, R.M., K. Shanmugam and I. Dinstein. 1973.  Textural Features for
    * Image Classification. IEEE Transactions on Systems, Man and Cybernetics.
    * SMC-3(6):610-620.
    *
    * Haralick, R.M. 1979. Statistical and Structural Approaches to Texture.
    * Proceedings of the IEEE, 67:786-804.
    *
    * R.W. Conners and C.A. Harlow. A Theoretical Comaprison of Texture Algorithms.
    * IEEE Transactions on Pattern Analysis and Machine Intelligence,  2:204-222, 1980.
    *
    * R.W. Conners, M.M. Trivedi, and C.A. Harlow. Segmentation of a High-Resolution
    * Urban Scene using Texture  Operators. Computer Vision, Graphics and Image
    * Processing, 25:273-310,  1984.
    *
    * \sa ScalarImageToCooccurrenceMatrixFilter
    * \sa ScalarImageToTextureFeaturesFilter
    *
    * Author: Zachary Pincus
    * \ingroup ITKStatistics
    */

    template< typename THistogram >
    class EnhancedHistogramToTextureFeaturesFilter:public ProcessObject
    {
    public:
      /** Standard typedefs */
      typedef EnhancedHistogramToTextureFeaturesFilter Self;
      typedef ProcessObject                    Superclass;
      typedef SmartPointer< Self >             Pointer;
      typedef SmartPointer< const Self >       ConstPointer;

      /** Run-time type information (and related methods). */
      itkTypeMacro(EnhancedHistogramToTextureFeaturesFilter, ProcessObject);

      /** standard New() method support */
      itkNewMacro(Self);

      typedef THistogram                                    HistogramType;
      typedef typename HistogramType::Pointer               HistogramPointer;
      typedef typename HistogramType::ConstPointer          HistogramConstPointer;
      typedef typename HistogramType::MeasurementType       MeasurementType;
      typedef typename HistogramType::MeasurementVectorType MeasurementVectorType;
      typedef typename HistogramType::IndexType             IndexType;
      typedef typename HistogramType::AbsoluteFrequencyType AbsoluteFrequencyType;
      typedef typename HistogramType::RelativeFrequencyType RelativeFrequencyType;

      typedef typename HistogramType::TotalAbsoluteFrequencyType
        TotalAbsoluteFrequencyType;

      typedef typename HistogramType::TotalRelativeFrequencyType
        TotalRelativeFrequencyType;

      /** Container to hold relative frequencies of the histogram */
      typedef std::vector< RelativeFrequencyType > RelativeFrequencyContainerType;

      /** Method to Set/Get the input Histogram */
      using Superclass::SetInput;
      void SetInput(const HistogramType *histogram);

      const HistogramType * GetInput() const;

      /** Smart Pointer type to a DataObject. */
      typedef DataObject::Pointer DataObjectPointer;

      /** Type of DataObjects used for scalar outputs */
      typedef SimpleDataObjectDecorator< MeasurementType > MeasurementObjectType;

      /** Return energy texture value. */
      MeasurementType GetEnergy() const;

      const MeasurementObjectType * GetEnergyOutput() const;

      /** Return entropy texture value. */
      MeasurementType GetEntropy() const;

      const MeasurementObjectType * GetEntropyOutput() const;

      /** return correlation texture value. */
      MeasurementType GetCorrelation() const;

      const MeasurementObjectType * GetCorrelationOutput() const;

      /** Return inverse difference moment texture value. */
      MeasurementType GetInverseDifferenceMoment() const;

      const MeasurementObjectType * GetInverseDifferenceMomentOutput() const;

      /** Return inertia texture value. */
      MeasurementType GetInertia() const;

      const MeasurementObjectType * GetInertiaOutput() const;

      /** Return cluster shade texture value. */
      MeasurementType GetClusterShade() const;

      const MeasurementObjectType * GetClusterShadeOutput() const;

      /** Return cluster prominence texture value. */
      MeasurementType GetClusterProminence() const;

      const MeasurementObjectType * GetClusterProminenceOutput() const;

      /** Return Haralick correlation texture value. */
      MeasurementType GetHaralickCorrelation() const;

      const MeasurementObjectType * GetHaralickCorrelationOutput() const;

      itkMacroGLCMFeatureGetter(Autocorrelation);
      itkMacroGLCMFeatureGetter(Contrast);
      itkMacroGLCMFeatureGetter(Dissimilarity);
      itkMacroGLCMFeatureGetter(MaximumProbability);
      itkMacroGLCMFeatureGetter(InverseVariance);
      itkMacroGLCMFeatureGetter(Homogeneity1);
      itkMacroGLCMFeatureGetter(ClusterTendency);
      itkMacroGLCMFeatureGetter(Variance);
      itkMacroGLCMFeatureGetter(SumAverage);
      itkMacroGLCMFeatureGetter(SumEntropy);
      itkMacroGLCMFeatureGetter(SumVariance);
      itkMacroGLCMFeatureGetter(DifferenceAverage);
      itkMacroGLCMFeatureGetter(DifferenceEntropy);
      itkMacroGLCMFeatureGetter(DifferenceVariance);
      itkMacroGLCMFeatureGetter(InverseDifferenceMomentNormalized);
      itkMacroGLCMFeatureGetter(InverseDifferenceNormalized);
      itkMacroGLCMFeatureGetter(InverseDifference);
      itkMacroGLCMFeatureGetter(JointAverage);
      itkMacroGLCMFeatureGetter(FirstMeasureOfInformationCorrelation);
      itkMacroGLCMFeatureGetter(SecondMeasureOfInformationCorrelation);

      /** Texture feature types */
      typedef enum {
        Energy,
        Entropy,
        Correlation,
        InverseDifferenceMoment,
        Inertia,
        ClusterShade,
        ClusterProminence,
        HaralickCorrelation,
        Autocorrelation,
        Contrast,
        Dissimilarity,
        MaximumProbability,
        InverseVariance,
        Homogeneity1,
        ClusterTendency,
        Variance,
        SumAverage,
        SumEntropy,
        SumVariance,
        DifferenceAverage,
        DifferenceEntropy,
        DifferenceVariance,
        InverseDifferenceMomentNormalized,
        InverseDifferenceNormalized,
        InverseDifference,
        JointAverage,
        FirstMeasureOfInformationCorrelation,
        SecondMeasureOfInformationCorrelation,
        InvalidFeatureName
      }  TextureFeatureName;

      /** convenience method to access the texture values */
      MeasurementType GetFeature(TextureFeatureName name);

    protected:
      EnhancedHistogramToTextureFeaturesFilter();
      ~EnhancedHistogramToTextureFeaturesFilter() override {}
      void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;

      /** Make a DataObject to be used for output output. */
      typedef ProcessObject::DataObjectPointerArraySizeType DataObjectPointerArraySizeType;
      using Superclass::MakeOutput;
      DataObjectPointer MakeOutput(DataObjectPointerArraySizeType) ITK_OVERRIDE;

      void GenerateData() ITK_OVERRIDE;

    private:
      EnhancedHistogramToTextureFeaturesFilter(const Self &); //purposely not implemented
      void operator=(const Self &);                   //purposely not implemented

      void ComputeMeansAndVariances(double & pixelMean, double & marginalMean,
        double & marginalDevSquared, double & pixelVariance);

      RelativeFrequencyContainerType m_RelativeFrequencyContainer;
    };
  } // end of namespace Statistics
} // end of namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkEnhancedHistogramToTextureFeaturesFilter.hxx"
#endif

#endif
